The incident was sparked in the final seconds when Lanus teenager Leandro Diaz kicked Universitario goalkeeper Raul Fernandez when he was on the ground after a making save, believing he was time-wasting.
Members of the Universitario bench also clashed with Lanus supporters after a fan jumped from the stands and appeared to try to take something from their dugout.
The result left Universitario in second place in Group Four behind Libertad of Paraguay, who secured their berth in the knockout phase with a 2-1 win over Blooming of Bolivia.
Libertad finished on 12 points from six matches with Universitario, on 10, hoping to go through as one of the six best second-placed teams from the eight groups.
Lanus, who risk sanctions from the South American Football Confederation over the incidents, ended with eight points and Blooming one.
Argentina's Velez Sarsfield went through as Group Seven winners after beating Deportivo Italia of Venezuela 4-0 at home with two goals from Uruguay striker Rodrigo Lopez.
Velez finished on 13 points, two ahead of Brazil's Cruzeiro, who drew 1-1 at Colo Colo of Chile in Santiago. Colo Colo, whose Uruguayan defender Andres Scotti was sent off in the 80th minute, took eight points and Italia one.
Group One leaders Corinthians, aiming to win the title for the first time in their centenary year, and Universidad de Chile, top of Group Eight, qualified on Wednesday with a match to spare. There is one round to go in those groups next week.
